If areas were affected by smoke, people should wipe down surfaces used for cooking and food preparation before using.
Anyone with shortness of breath or worsening of asthma symptoms was urged to see their doctor.
Dr Guy Coulson, Niwa's science leader for air-quality research, said scientists would be trying to ascertain the chemical composition of the smoke – and how much of it there still was.
While some might have turned to wearing face masks, Coulson's message was for people to avoid coming near the smoke in the first place.
Although he expected a localised peak in poor air quality around the city centre, the picture could be back to normal in days.
"We can probably look at this as a short-term event that will last one or two days – after the fire has stopped, everything will return to normal fairly quickly," Coulson said.
"What's in the air will be blown away. Its long-term impact probably won't be distinguishable and it will be back to business as usual."
Coulson pointed out that Auckland's CBD did include many small valleys where smoke might persist – and this would have been the case had the fire occurred in winter.
"But we've got very strong wind today – we are talking about gusts of 100km/h – so I'd expect it will disperse very quickly."
Coulson said there may be interest in capturing and measuring microplastic particles in the air as a result of the fire.
"But measuring that is not quite so easy, as we are only at the beginning of being able to do that."
